Big refactor here

- rename packages -> bio4j/bio4j#28
- rename core classes as in bio4j/bio4j#24

I made Vertex and Edge concrete classes for simplicity; probably all
the implementing subclasses should be made final.

It would be a good idea to review return types.
no LICENSE headers, fix abstract classes, update wrt model
review code, make all classes final whenever possible
Merge branch 'master' into refactor/node/vertex/classes

NO conflicts!
Merge branch 'refactor/node/vertex/classes'